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comparison rsem_prepare_reference.xml @ 2:f6b8155ab12a

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Add test cases
author Jim Johnson <jj@umn.edu>
date Thu, 06 Feb 2014 11:46:40 -0600
parents 1ff2fc8da328
children d7d4d662b0e9
comparison
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1:1ff2fc8da328 2:f6b8155ab12a
30 --gtf $reference.gtf 30 --gtf $reference.gtf
31 $reference.reference_fasta_file 31 $reference.reference_fasta_file
32 #end if 32 #end if
33 $reference_name 33 $reference_name
34 </command> 34 </command>
35
36 <inputs> 35 <inputs>
37 <conditional name="reference"> 36 <conditional name="reference">
38 <param name="ref_type" type="select" label=""> 37 <param name="ref_type" type="select" label="Reference transcript source">
39 <option value="transcripts">transcript fasta</option> 38 <option value="transcripts">transcript fasta</option>
40 <option value="genomic">reference genome and gtf</option> 39 <option value="genomic">reference genome and gtf</option>
41 </param> 40 </param>
42 <when value="transcripts"> 41 <when value="transcripts">
43 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" 42 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
44 help="The files should contain the sequences of transcripts."/> 43 help="The files should contain the sequences of transcripts."/>
45
46 </when> 44 </when>
47 <when value="genomic"> 45 <when value="genomic">
48 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" 46 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
49 help="The files should contain either the sequences of an entire genome."/> 47 help="The file should contain the sequence of an entire genome."/>
50 <param name="gtf" type="data" format="gtf" optional="true" label="gtf" 48 <param name="gtf" type="data" format="gtf" label="gtf"
51 help="extract transcript reference sequences using the gene annotations specified in this GTF" /> 49 help="extract transcript reference sequences using the gene annotations specified in this GTF" />
52 </when> 50 </when>
53 </conditional> 51 </conditional>
54 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > 52 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
55 <help> 53 <help>
60 Without a map: 58 Without a map:
61 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. 59 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
62 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene. 60 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
63 </help> 61 </help>
64 </param> 62 </param>
65 <param name="reference_name" type="text" value="" label="reference name"> 63 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
64 <help>A one work name for this RSEM reference containing only letters, digits, and underscore characters</help>
65 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
66 </param> 66 </param>
67
68 <conditional name="polya"> 67 <conditional name="polya">
69 <param name="polya_use" type="select" label="PolyA "> 68 <param name="polya_use" type="select" label="PolyA ">
70 <option value="add" selected="true">Add poly(A) tails to all transcripts</option> 69 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
71 <option value="subset">Exclude poly(A) tails from selected transcripts</option> 70 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
72 <option value="none">Do not add poly(A) tails to any transcripts</option> 71 <option value="none">Do not add poly(A) tails to any transcripts</option>
82 <validator type="in_range" message="must be positive " min="1"/> 81 <validator type="in_range" message="must be positive " min="1"/>
83 </param> 82 </param>
84 </when> 83 </when>
85 <when value="none"/> 84 <when value="none"/>
86 </conditional> 85 </conditional>
87
88 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/> 86 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/>
89 </inputs> 87 </inputs>
90 <stdio> 88 <stdio>
91 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> 89 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
92 </stdio> 90 </stdio>
93 <outputs> 91 <outputs>
94 <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/> 92 <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/>
95 </outputs> 93 </outputs>
94 <tests>
95 <test>
96 <param name="ref_type" value="genomic"/>
97 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
98 <param name="gtf" value="ref.gtf" ftype="gtf"/>
99 <param name="reference_name" value="ref"/>
100 </test>
101 </tests>
96 <help> 102 <help>
97
98 103
99 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ 104 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
100 105
101 NAME 106 NAME
102 rsem-prepare-reference 107 rsem-prepare-reference
107 DESCRIPTION 112 DESCRIPTION
108 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters. 113 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
109 This program is used in conjunction with the 'rsem-calculate-expression' program. 114 This program is used in conjunction with the 'rsem-calculate-expression' program.
110 115
111 INPUTS 116 INPUTS
112 117 A fasta file of transcripts
113 118 or
119 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)
114 120
115 </help> 121 </help>
116 </tool> 122 </tool>